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Structure-activity relationships at the 5-position of thiolactomycin: an intact 5(R)-isoprene unit is required for activity against the condensing enzymes from Mycobacterium tuberculosis and Escherchia coli
Starting Model(s) Initial Refinement Model(s) Type Source Accession Code Details experimental model PDB 1FJ4 PDB ENTRY 1FJ4
Crystallization Crystalization Experiments ID Method pH Temperature Details 1 VAPOR DIFFUSION, HANGING DROP 7.5 290 1.9 M Ammonium Sulfate, 0.1 M HEPES pH 7.5, 2% PEG400, VAPOR DIFFUSION, HANGING DROP, temperature 290K
Crystal Properties Matthews coefficient Solvent content 2.5 50.6
Crystal Data Unit Cell Length ( Å ) Angle ( ˚ ) a = 59.104 α = 90 b = 139.193 β = 90 c = 212.326 γ = 90
Symmetry Space Group P 21 21 21
Diffraction Diffraction Experiment ID # Crystal ID Scattering Type Data Collection Temperature Detector Detector Type Details Collection Date Monochromator Protocol 1 1 x-ray 170 CCD BRUKER 2005-07-11 M SINGLE WAVELENGTH
Radiation Source ID # Source Type Wavelength List Synchrotron Site Beamline 1 ROTATING ANODE BRUKER
Data Collection Overall ID # Resolution (High) Resolution (Low) Percent Possible (Observed) R Merge I (Observed) Net I Over Average Sigma (I) Redundancy Number Reflections (All) Number Reflections (Observed) Observed Criterion Sigma (F) Observed Criterion Sigma (I) B (Isotropic) From Wilson Plot 1 2.2 40 99.5 0.077 18.6 6.8 90238 90238 15.5
Highest Resolution Shell ID # Resolution (High) Resolution (Low) Percent Possible (All) Percent Possible (Observed) R Merge I (Observed) Mean I Over Sigma (Observed) Redundancy Number Unique Reflections (All) 2.2 2.3 98 0.182 5
Refinement Statistics Diffraction ID Structure Solution Method Cross Validation method Starting model Resolution (High) Resolution (Low) Cut-off Sigma (F) Number Reflections (All) Number Reflections (Observed) Number Reflections (R-Free) Percent Reflections (Observed) R-Factor (All) R-Factor (Observed) R-Work (Depositor) R-Free (Depositor) R-Free (DCC) R-Free Selection Details Mean Isotropic B X-RAY DIFFRACTION MOLECULAR REPLACEMENT THROUGHOUT PDB ENTRY 1FJ4 2.19 40 2 90238 85651 4519 99.55 0.196 0.19597 0.19446 0.22468 0.1907 RANDOM 15.468
Temperature Factor Modeling Anisotropic B[1][1] Anisotropic B[1][2] Anisotropic B[1][3] Anisotropic B[2][2] Anisotropic B[2][3] Anisotropic B[3][3] -0.16 0.74 -0.58
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.928 r_dihedral_angle_4_deg 20.606 r_dihedral_angle_3_deg 16.248 r_dihedral_angle_1_deg 5.442 r_scangle_it 1.793 r_angle_refined_deg 1.156 r_scbond_it 1.096 r_mcangle_it 0.702 r_mcbond_it 0.404 r_nbtor_refined 0.294
RMS Deviations Key Refinement Restraint Deviation r_dihedral_angle_2_deg 36.928 r_dihedral_angle_4_deg 20.606 r_dihedral_angle_3_deg 16.248 r_dihedral_angle_1_deg 5.442 r_scangle_it 1.793 r_angle_refined_deg 1.156 r_scbond_it 1.096 r_mcangle_it 0.702 r_mcbond_it 0.404 r_nbtor_refined 0.294 r_nbd_refined 0.19 r_symmetry_vdw_refined 0.156 r_symmetry_hbond_refined 0.147 r_xyhbond_nbd_refined 0.125 r_chiral_restr 0.078 r_bond_refined_d 0.008 r_gen_planes_refined 0.003
Non-Hydrogen Atoms Used in Refinement Non-Hydrogen Atoms Number Protein Atoms 11825 Nucleic Acid Atoms Solvent Atoms 537 Heterogen Atoms 39
Software Software Software Name Purpose REFMAC refinement SAINT data reduction LSCALE data scaling AMoRE phasing